Well, glad to know it was straight forward.
Thing is, I run every STL through my Netfabb so I didn't think to check in S3D for multiple meshes!
Turns out I had the Auto Repair off from last importing a complex model that would crash Netfabb on Auto Repair so alas when I saved this model it was still 2 meshes!

Glad it wasn't actually a "bug" and was just me forgetting to double check my process.